The functionality of a protein depends on its correct folding, but newly synthesized proteins are susceptible to aberrant folding and aggregation. Heat shock proteins (HSPs) function as molecular chaperones that aid in protein folding and the degradation of misfolded proteins. Trinucleotide (CAG) repeat expansion in the Huntingtin gene (HTT) results in the expression of misfolded Huntingtin protein (Htt), which contributes to the development of Huntington's disease. We previously found that... Show moreThe functionality of a protein depends on its correct folding, but newly synthesized proteins are susceptible to aberrant folding and aggregation. Heat shock proteins (HSPs) function as molecular chaperones that aid in protein folding and the degradation of misfolded proteins. Trinucleotide (CAG) repeat expansion in the Huntingtin gene (HTT) results in the expression of misfolded Huntingtin protein (Htt), which contributes to the development of Huntington's disease. We previously found that the degradation of mutated Htt with polyQ expansion (Htt103QP) depends on both ubiquitin proteasome system and autophagy. However, the role of heat shock proteins in the clearance of mutated Htt remains poorly understood. Here, we report that cytosolic Hsp70 (Ssa family), its nucleotide exchange factors (Sse1 and Fes1), and a Hsp40 co-chaperone (Ydj1) are required for inclusion body formation of Htt103QP proteins and their clearance via autophagy. Extended induction of Htt103QPGFP leads to the formation of a single inclusion body in wild-type yeast cells, but mutant cells lacking these HSPs exhibit increased number of Htt103QP aggregates. Most notably, we detected more aggregated forms of Htt103QP in sse1 Delta. mutant cells using an agarose gel assay. Increased protein aggregates are also observed in these HSP mutants even in the absence Htt103QP overexpression. Importantly, these HSPs are required for autophagy- mediated Htt103QP clearance, but are less critical for proteasome-dependent degradation. These findings suggest a chaperone network that facilitates inclusion body formation of misfolded proteins and the subsequent autophagic clearance. Show less

Date Issued

2018-01-18

Identifier

FSU_libsubv1_wos_000422749500056, 10.1371/journal.pone.0191490

Format

Citation

Title

Attention And Working Memory Deficits In A Perinatal Nicotine Exposure Mouse Model.

Creator

Zhang, Lin, Spencer, Thomas J., Biederman, Joseph, Bhide, Pradeep G.

Abstract/Description

Background Cigarette smoking by pregnant women is associated with a significant increase in the risk for cognitive disorders in their children. Preclinical models confirm this risk by showing that exposure of the developing brain to nicotine produces adverse behavioral outcomes. Here we describe behavioral phenotypes resulting from perinatal nicotine exposure in a mouse model, and discuss our findings in the context of findings from previously published studies using preclinical models of... Show moreBackground Cigarette smoking by pregnant women is associated with a significant increase in the risk for cognitive disorders in their children. Preclinical models confirm this risk by showing that exposure of the developing brain to nicotine produces adverse behavioral outcomes. Here we describe behavioral phenotypes resulting from perinatal nicotine exposure in a mouse model, and discuss our findings in the context of findings from previously published studies using preclinical models of developmental nicotine exposure. Methodology/Principal findings Female C57BI/6 mice received drinking water containing nicotine (100pg/ml) + saccharin (2%) starting 3 weeks prior to breeding and continuing throughout pregnancy, and until 3 weeks postpartum. Over the same period, female mice in two control groups received drinking water containing saccharin (2%) or plain drinking water. Offspring from each group were weaned at 3-weeks of age and subjected to behavioral analyses at 3 months of age. We examined spontaneous locomotor activity, anxiety-like behavior, spatial working memory, object based attention, recognition memory and impulsive-like behavior. We found significant deficits in attention and working memory only in male mice, and no significant changes in the other behavioral phenotypes in male or female mice. Exposure to saccharin alone did not produce significant changes in either sex. Conclusion/Significance The perinatal nicotine exposure produced significant deficits in attention and working memory in a sex-dependent manner in that the male but not female offspring displayed these behaviors. These behavioral phenotypes are associated with attention deficit hyperactivity disorder (ADHD) and have been reported in other studies that used pre-or perinatal nicotine exposure. Therefore, we suggest that preclinical models of developmental nicotine exposure could be useful tools for modeling ADHD and related disorders. Show less

Here, we present a mechanistically grounded theory detailing a novel function of the behavioral immune system (BIS), the psychological system that prompts pathogen avoidance behaviors. We propose that BIS activity allows the body to downregulate basal inflammation, preventing resultant oxidative damage to DNA and promoting longevity. Study 1 investigated the relationship between a trait measure of pathogen avoidance motivation and in vitro and in vivo proinflammatory cytokine production.... Show moreHere, we present a mechanistically grounded theory detailing a novel function of the behavioral immune system (BIS), the psychological system that prompts pathogen avoidance behaviors. We propose that BIS activity allows the body to downregulate basal inflammation, preventing resultant oxidative damage to DNA and promoting longevity. Study 1 investigated the relationship between a trait measure of pathogen avoidance motivation and in vitro and in vivo proinflammatory cytokine production. Study 2 examined the relationship between this same predictor and DNA damage often associated with prolonged inflammation. Results revealed that greater trait pathogen avoidance motivation predicts a) lower levels of spontaneous (but not stimulated) proinflammatory cytokine release by peripheral blood mononuclear cells (PBMCs), b) lower plasma levels of the proinflammatory cytokine interleukin-6 (IL-6), and c) lower levels of oxidative DNA damage. Thus, the BIS may promote health by protecting the body from the deleterious effects of inflammation and oxidative stress. Show less

Date Issued

2018-09-20

Identifier

FSU_libsubv1_wos_000445626400047, 10.1371/journal.pone.0203961

Format

Citation

Title

Bias Caused By Sampling Error In Meta-analysis With Small Sample Sizes.

Creator

Lin, Lifeng

Abstract/Description

Background Meta-analyses frequently include studies with small sample sizes. Researchers usually fail to account for sampling error in the reported within-study variances; they model the observed study-specific effect sizes with the within-study variances and treat these sample variances as if they were the true variances. However, this sampling error may be influential when sample sizes are small. This article illustrates that the sampling error may lead to substantial bias in meta-analysis... Show moreBackground Meta-analyses frequently include studies with small sample sizes. Researchers usually fail to account for sampling error in the reported within-study variances; they model the observed study-specific effect sizes with the within-study variances and treat these sample variances as if they were the true variances. However, this sampling error may be influential when sample sizes are small. This article illustrates that the sampling error may lead to substantial bias in meta-analysis results. Methods We conducted extensive simulation studies to assess the bias caused by sampling error. Meta-analyses with continuous and binary outcomes were simulated with various ranges of sample size and extents of heterogeneity. We evaluated the bias and the confidence interval coverage for five commonly-used effect sizes (i.e., the mean difference, standardized mean difference, odds ratio, risk ratio, and risk difference). Results Sampling error did not cause noticeable bias when the effect size was the mean difference, but the standardized mean difference, odds ratio, risk ratio, and risk difference suffered from this bias to different extents. The bias in the estimated overall odds ratio and risk ratio was noticeable even when each individual study had more than 50 samples under some settings. Also, Hedges' g, which is a bias-corrected estimate of the standardized mean difference within studies, might lead to larger bias than Cohen's d in meta-analysis results. Conclusions Cautions are needed to perform meta-analyses with small sample sizes. The reported within-study variances may not be simply treated as the true variances, and their sampling error should be fully considered in such meta-analyses. Show less

Some species of butterflyfish have had preyed upon corals for millions of years, yet the mechanism of butterflyfish specialized coral feeding strategy remains poorly understood. Certain butterflyfish have the ability to feed on allelochemically rich soft corals, e.g. Sinularia maxima. Cytochrome P450 (CYP) is the predominant enzyme system responsible for the detoxification of dietary allelochemicals. CYP2-like and CYP3A-like content have been associated with butterflyfish that preferentially... Show moreSome species of butterflyfish have had preyed upon corals for millions of years, yet the mechanism of butterflyfish specialized coral feeding strategy remains poorly understood. Certain butterflyfish have the ability to feed on allelochemically rich soft corals, e.g. Sinularia maxima. Cytochrome P450 (CYP) is the predominant enzyme system responsible for the detoxification of dietary allelochemicals. CYP2-like and CYP3A-like content have been associated with butterflyfish that preferentially consumes allelochemically rich soft corals. To investigate the role of butterflyfish CYP2 and CYP3A enzymes in dietary preference, we conducted oral feeding experiments using homogenates of S. maxima and a toxin isolated from the coral in four species of butterflyfish with different feeding strategies. After oral exposure to the S. maxima toxin 5-episinulaptolide (5ESL), which is not normally encountered in the Hawaiian butterflyfish diet, an endemic specialist, Chaetodon multicinctus experienced 100% mortality compared to a generalist, Chaetodon auriga, which had significantly more (3-6 fold higher) CYP3A-like basal content and catalytic activity. The specialist, Chaetodon unimaculatus, which preferentially feed on S. maxima in Guam, but not in Hawaii, had 100% survival, a significant induction of 8-12 fold CYP3A-like content, and an increased ability (2-fold) to metabolize 5ESL over other species. Computer modeling data of CYP3A4 with 5ESL were consistent with microsomal transformation of 5ESL to a C15-16 epoxide from livers of C. unimaculatus. Epoxide formation correlated with CYP3A-like content, catalytic activity, induction, and NADPH-dependent metabolism of 5ESL. These results suggest a potentially important role for the CYP3A family in butterflyfish-coral diet selection through allelochemical detoxification. Show less

Soil invertebrates such as ants are thought to be important manipulators of soils in temperate and tropical ecosystems. The fungus gardening ant, Trachymyrmex septentrionalis, is an important agent of biomantling, that is, of depositing soil excavated from below onto the surface, and has been suggested as an agent of bioturbation (moving soil below ground) as well. The amount of bioturbation by this ant was quantified by planting queenright colonies in sand columns consisting of 5 layers of... Show moreSoil invertebrates such as ants are thought to be important manipulators of soils in temperate and tropical ecosystems. The fungus gardening ant, Trachymyrmex septentrionalis, is an important agent of biomantling, that is, of depositing soil excavated from below onto the surface, and has been suggested as an agent of bioturbation (moving soil below ground) as well. The amount of bioturbation by this ant was quantified by planting queenright colonies in sand columns consisting of 5 layers of different colored sand. The amount of each color of sand deposited on the surface was determined from April to November 2015. In November, colonies were excavated and the color and amount of sand deposited below ground (mostly as backfill in chambers) was determined. Extrapolated to one ha, T. septentrionalis deposited 800 kg of sand per annum on the surface, and an additional 200 kg (17% of the total excavated) below ground. On average, this mixes 1.3% of the sand from other layers within the top meter of soil per millennium, but this mixing is unlikely to be homogeneous, and probably occurs as "hotspots" in both horizontal and vertical space. Such mixing is discussed as a challenge to sediment dating by optically stimulated luminescence (OSL). Show less

Date Issued

2016-07-08

Identifier

FSU_libsubv1_wos_000380005400162, 10.1371/journal.pone.0158920

Format

Citation

Title

Carbon Abatement and Emissions Associated with the Gasification of Walnut Shells for Bioenergy and Biochar Production.

Creator

Pereira, Engil Isadora Pujol, Suddick, Emma C., Six, Johan

Abstract/Description

By converting biomass residue to biochar, we could generate power cleanly and sequester carbon resulting in overall greenhouse gas emissions (GHG) savings when compared to typical fossil fuel usage and waste disposal. We estimated the carbon dioxide (CO2) abatements and emissions associated to the concurrent production of bioenergy and biochar through biomass gasification in an organic walnut farm and processing facility in California, USA. We accounted for (i) avoided-CO2 emissions from... Show moreBy converting biomass residue to biochar, we could generate power cleanly and sequester carbon resulting in overall greenhouse gas emissions (GHG) savings when compared to typical fossil fuel usage and waste disposal. We estimated the carbon dioxide (CO2) abatements and emissions associated to the concurrent production of bioenergy and biochar through biomass gasification in an organic walnut farm and processing facility in California, USA. We accounted for (i) avoided-CO2 emissions from displaced grid electricity by bioenergy; (ii) CO2 emissions from farm machinery used for soil amendment of biochar; (iii) CO2 sequestered in the soil through stable biochar-C; and (iv) direct CO2 and nitrous oxide (N2O) emissions from soil. The objective of these assessments was to pinpoint where the largest C offsets can be expected in the bioenergy-biochar chain. We found that energy production from gasification resulted in 91.8% of total C offsets, followed by stable biochar-C (8.2% of total C sinks), offsetting a total of 107.7 kg CO2-C eq Mg-1 feedstock. At the field scale, we monitored gas fluxes from soils for 29 months (180 individual observations) following field management and precipitation events in addition to weekly measurements within three growing seasons and two tree dormancy periods. We compared four treatments: control, biochar, compost, and biochar combined with compost. Biochar alone or in combination with compost did not alter total N2O and CO2 emissions from soils, indicating that under the conditions of this study, biochar-prompted C offsets may not be expected from the mitigation of direct soil GHG emissions. However, this study revealed a case where a large environmental benefit was given by the waste-to-bioenergy treatment, addressing farm level challenges such as waste management, renewable energy generation, and C sequestration. Show less

Circadian clocks impact vital cardiac parameters such as blood pressure and heart rate, and adverse cardiac events such as myocardial infarction and sudden cardiac death. In mammals, the central circadian pacemaker, located in the suprachiasmatic nucleus of the hypothalamus, synchronizes cellular circadian clocks in the heart and many other tissues throughout the body. Cardiac ventricle explants maintain autonomous contractions and robust circadian oscillations of clock gene expression in... Show moreCircadian clocks impact vital cardiac parameters such as blood pressure and heart rate, and adverse cardiac events such as myocardial infarction and sudden cardiac death. In mammals, the central circadian pacemaker, located in the suprachiasmatic nucleus of the hypothalamus, synchronizes cellular circadian clocks in the heart and many other tissues throughout the body. Cardiac ventricle explants maintain autonomous contractions and robust circadian oscillations of clock gene expression in culture. In the present study, we examined the relationship between intrinsic myocardial function and circadian rhythms in cultures from mouse heart. We cultured ventricular explants or dispersed cardiomyocytes from neonatal mice expressing a PER2::LUC bioluminescent reporter of circadian clock gene expression. We found that isoproterenol, a beta-adrenoceptor agonist known to increase heart rate and contractility, also amplifies PER2 circadian rhythms in ventricular explants. We found robust, cell-autonomous PER2 circadian rhythms in dispersed cardiomyocytes. Single-cell rhythms were initially synchronized in ventricular explants but desynchronized in dispersed cells. In addition, we developed a method for long-term, simultaneous monitoring of clock gene expression, contraction rate, and basal intracellular Ca2+ level in cardiomyocytes using PER2:: LUC in combination with GCaMP3, a genetically encoded fluorescent Ca2+ reporter. In contrast to robust PER2 circadian rhythms in cardiomyocytes, we detected no rhythms in contraction rate and only weak rhythms in basal Ca2+ level. In summary, we found that PER2 circadian rhythms of cardiomyocytes are cell-autonomous, amplified by adrenergic signaling, and synchronized by intercellular communication in ventricle explants, but we detected no robust circadian rhythms in contraction rate or basal Ca2+. Show less

Date Issued

2016-07-26

Identifier

FSU_libsubv1_wos_000381515600037, 10.1371/journal.pone.0159618

Format

Citation

Title

Chronic Methamphetamine Effects on Brain Structure and Function in Rats.

Methamphetamine (MA) addiction is a growing epidemic worldwide. Chronic MA use has been shown to lead to neurotoxicity in rodents and humans. Magnetic resonance imaging (MRI) studies in MA users have shown enlarged striatal volumes and positron emission tomography (PET) studies have shown decreased brain glucose metabolism (BGluM) in the striatum of detoxified MA users. The present study examines structural changes of the brain, observes microglial activation, and assesses changes in brain... Show moreMethamphetamine (MA) addiction is a growing epidemic worldwide. Chronic MA use has been shown to lead to neurotoxicity in rodents and humans. Magnetic resonance imaging (MRI) studies in MA users have shown enlarged striatal volumes and positron emission tomography (PET) studies have shown decreased brain glucose metabolism (BGluM) in the striatum of detoxified MA users. The present study examines structural changes of the brain, observes microglial activation, and assesses changes in brain function, in response to chronic MA treatment. Rats were randomly split into three distinct treatment groups and treated daily for four months, via i.p. injection, with saline (controls), or low dose (LD) MA (4 mg/kg), or high dose (HD) MA (8 mg/kg). Sixteen weeks into the treatment period, rats were injected with a glucose analog, [F-18] fluorodeoxyglucose (FDG), and their brains were scanned with micro-PET to assess regional BGluM. At the end of MA treatment, magnetic resonance imaging at 21T was performed on perfused rats to determine regional brain volume and in vitro [H-3]PK 11195 autoradiography was performed on fresh-frozen brain tissue to measure microglia activation. When compared with controls, chronic HD MA-treated rats had enlarged striatal volumes and increases in [H-3]PK 11195 binding in striatum, the nucleus accumbens, frontal cortical areas, the rhinal cortices, and the cerebellar nuclei. FDG microPET imaging showed that LD MA-treated rats had higher BGluM in insular and somatosensory cortices, face sensory nucleus of the thalamus, and brainstem reticular formation, while HD MA-treated rats had higher BGluM in primary and higher order somatosensory and the retrosplenial cortices, compared with controls. HD and LD MA-treated rats had lower BGluM in the tail of the striatum, rhinal cortex, and subiculum and HD MA also had lower BGluM in hippocampus than controls. These results corroborate clinical findings and help further examine the mechanisms behind MA-induced neurotoxicity. Show less

Date Issued

2016-06-08

Identifier

FSU_libsubv1_wos_000377561700005, 10.1371/journal.pone.0155457

Format

Citation

Title

A Critical Evaluation of the Down Syndrome Diagnosis for LB1, Type Specimen of Homo floresiensis.

The Liang Bua hominins from Flores, Indonesia, have been the subject of intense scrutiny and debate since their initial description and classification in 2004. These remains have been assigned to a new species, Homo floresiensis, with the partial skeleton LB1 as the type specimen. The Liang Bua hominins are notable for their short stature, small endocranial volume, and many features that appear phylogenetically primitive relative to modern humans, despite their late Pleistocene age. Recently,... Show moreThe Liang Bua hominins from Flores, Indonesia, have been the subject of intense scrutiny and debate since their initial description and classification in 2004. These remains have been assigned to a new species, Homo floresiensis, with the partial skeleton LB1 as the type specimen. The Liang Bua hominins are notable for their short stature, small endocranial volume, and many features that appear phylogenetically primitive relative to modern humans, despite their late Pleistocene age. Recently, some workers suggested that the remains represent members of a small-bodied island population of modern Austro-Melanesian humans, with LB1 exhibiting clinical signs of Down syndrome. Many classic Down syndrome signs are soft tissue features that could not be assessed in skeletal remains. Moreover, a definitive diagnosis of Down syndrome can only be made by genetic analysis as the phenotypes associated with Down syndrome are variable. Most features that contribute to the Down syndrome phenotype are not restricted to Down syndrome but are seen in other chromosomal disorders and in the general population. Nevertheless, we re-evaluated the presence of those phenotypic features used to support this classification by comparing LB1 to samples of modern humans diagnosed with Down syndrome and euploid modern humans using comparative morphometric analyses. We present new data regarding neurocranial, brain, and symphyseal shape in Down syndrome, additional estimates of stature for LB1, and analyses of inter- and intralimb proportions. The presence of cranial sinuses is addressed using CT images of LB1. We found minimal congruence between the LB1 phenotype and clinical descriptions of Down syndrome. We present important differences between the phenotypes of LB1 and individuals with Down syndrome, and quantitative data that characterize LB1 as an outlier compared with Down syndrome and non-Down syndrome groups. Homo floresiensis remains a phenotypically unique, valid species with its roots in Plio-Pleistocene Homo taxa. Show less

Date Issued

2016-06-08

Identifier

FSU_libsubv1_wos_000377561700008, 10.1371/journal.pone.0155731

Format

Citation

Title

Demographics As Predictors Of Suicidal Thoughts And Behaviors: A Meta-analysis.

Background Certain demographic factors have long been cited to confer risk or protection for suicidal thoughts and behaviors. However, many studies have found weak or non-significant effects. Determining the effect strength and clinical utility of demographics as predictors is crucial for suicide risk assessment and theory development. As such, we conducted a meta-analysis to determine the effect strength and clinical utility of demographics as predictors. Methods We searched PsycInfo, PubMed... Show moreBackground Certain demographic factors have long been cited to confer risk or protection for suicidal thoughts and behaviors. However, many studies have found weak or non-significant effects. Determining the effect strength and clinical utility of demographics as predictors is crucial for suicide risk assessment and theory development. As such, we conducted a meta-analysis to determine the effect strength and clinical utility of demographics as predictors. Methods We searched PsycInfo, PubMed, and GoogleScholar for studies published before January 1st, 2015. Inclusion criteria required that studies use at least one demographic factor to longitudinally predict suicide ideation, attempt, or death. The initial search yielded 2,541 studies, 159 of which were eligible. A total of 752 unique statistical tests were included in analysis. Results Suicide death was the most commonly studied outcome, followed by attempt and ideation. The average follow-up length was 9.4 years. The overall effects of demographic factors studied in the field as risk factors were significant but weak, and that of demographic factors studied as protective factors were non-significant. Adjusting for publication bias further reduced effect estimates. No specific demographic factors appeared to be strong predictors. The effects were consistent across multiple moderators. Conclusions At least within the narrow methodological constraints of the existing literature, demographic factors were statistically significant risk factors, but not protective factors. Even as risk factors, demographics offer very little improvement in predictive accuracy. Future studies that go beyond the limitations of the existing literature are needed to further understand the effects of demographics. Show less

Dpb11 is required for the initiation of DNA replication in budding yeast. We found that Dpb11 binds tightly to single-stranded DNA (ssDNA) or branched DNA structures, while its human homolog, TopBP1, binds tightly to branched-DNA structures. We also found that Dpb11 binds stably to CDK-phosphorylated RPA, the eukaryotic ssDNA binding protein, in the presence of branched DNA. A Dpb11 mutant specifically defective for DNA binding did not exhibit tight binding to RPA in the presence of DNA,... Show moreDpb11 is required for the initiation of DNA replication in budding yeast. We found that Dpb11 binds tightly to single-stranded DNA (ssDNA) or branched DNA structures, while its human homolog, TopBP1, binds tightly to branched-DNA structures. We also found that Dpb11 binds stably to CDK-phosphorylated RPA, the eukaryotic ssDNA binding protein, in the presence of branched DNA. A Dpb11 mutant specifically defective for DNA binding did not exhibit tight binding to RPA in the presence of DNA, suggesting that Dpb11-interaction with DNA may promote the recruitment of RPA to melted DNA. We then characterized a mutant of Dpb11 that is specifically defective in DNA binding in budding yeast cells. Expression of dpb11-m1,2,3,5,Delta C results in a substantial decrease in RPA recruitment to origins, suggesting that Dpb11 interaction with DNA may be required for RPA recruitment to origins. Expression of dpb11-m1,2,3,5,Delta C also results in diminished GINS interaction with Mcm2-7 during S phase, while Cdc45 interaction with Mcm2-7 is like wild-type. The reduced GINS interaction with Mcm2-7 may be an indirect consequence of diminished origin melting. We propose that the tight interaction between Dpb11, CDK-phosphorylated RPA, and branched-DNA may be required for the essential function of stabilizing melted origin DNA in vivo. We also propose an alternative model, wherein Dpb11-DNA interaction is required for some other function in DNA replication initiation, such as helicase activation. Show less

Introduction African American (AA) women diagnosed with breast cancer are more likely to have aggressive subtypes. Investigating differentially expressed genes between patient populations may help explain racial health disparities. Resistin, one such gene, is linked to inflammation, obesity, and breast cancer risk. Previous studies indicated that resistin expression is higher in serum and tissue of AA breast cancer patients compared to Caucasian American (CA) patients. However, resistin... Show moreIntroduction African American (AA) women diagnosed with breast cancer are more likely to have aggressive subtypes. Investigating differentially expressed genes between patient populations may help explain racial health disparities. Resistin, one such gene, is linked to inflammation, obesity, and breast cancer risk. Previous studies indicated that resistin expression is higher in serum and tissue of AA breast cancer patients compared to Caucasian American (CA) patients. However, resistin expression levels have not been compared between AA and CA patients in a stage- and subtype-specific context. Breast cancer prognosis and treatments vary by subtype. This work investigates differential resistin gene expression in human breast cancer tissues of specific stages, receptor subtypes, and menopause statuses in AA and CA women. Methods Differential gene expression analysis was performed using human breast cancer gene expression data from The Cancer Genome Atlas. We performed inter-race resistin gene expression level comparisons looking at receptor status and stage-specific data between AA and CA samples. DESeq was run to test for differentially expressed resistin values. Results Resistin RNA was higher in AA women overall, with highest values in receptor negative subtypes. Estrogen-, progesterone-, and human epidermal growth factor receptor 2-negative groups showed statistically significant elevated resistin levels in Stage I and II AA women compared to CA women. In inter-racial comparisons, AA women had significantly higher levels of resistin regardless of menopause status. In whole population comparisons, resistin expression was higher among Stage I and III estrogen receptor negative cases. In comparisons of molecular subtypes, resistin levels were significant higher in triple negative than in luminal A breast cancer. Conclusion Resistin gene expression levels were significantly higher in receptor negative subtypes, especially estrogen receptor negative cases in AA women. Resistin may serve as an early breast cancer biomarker and possible therapeutic target for AA breast cancer. Show less

Date Issued

2016-06-17

Identifier

FSU_libsubv1_wos_000378030000048, 10.1371/journal.pone.0157741

Format

Citation

Title

An Experimental Study Of Turtle Shell Rattle Production And The Implications For Archaeofaunal Assemblages.

Creator

Gillreath-Brown, Andrew, Peres, Tanya M.

Abstract/Description

Turtle shell rattles are percussion instruments used by Indigenous peoples of the Americas in ceremonial contexts to keep rhythm. Archaeological investigations in the southeastern United States produced several complete and partial Eastern box turtle (Terrapene Carolina) shell rattles from mortuary contexts dating from the Archaic (ca. 8000-1000 BC) through Mississippian periods (ca. AD 800-1500). Fragmentary turtle remains, some identified as Eastern box turtle, are frequently recovered from... Show moreTurtle shell rattles are percussion instruments used by Indigenous peoples of the Americas in ceremonial contexts to keep rhythm. Archaeological investigations in the southeastern United States produced several complete and partial Eastern box turtle (Terrapene Carolina) shell rattles from mortuary contexts dating from the Archaic (ca. 8000-1000 BC) through Mississippian periods (ca. AD 800-1500). Fragmentary turtle remains, some identified as Eastern box turtle, are frequently recovered from non-mortuary contexts. Traditionally, these fragmentary remains are attributed to food waste. Given the archaeological and ethnographic evidence for turtle shell rattles, we need to consider how fragmentary remains might fit into the chaine operatoire of rattle production. This paper presents the results of an experimental study designed to identify one such chaine operatoire of rattle production. During this experiment, the data on taphonomic processes such as manufacturing marks, usewear, and breakage patterns, were recorded. We then tested the taphonomic findings from the experimental study and an object trait list we compiled from known rattle specimens and documentary sources with archaeological turtle remains recovered from non-mortuary contexts at two Mississippian period (ca. AD 1000-1450) sites in Middle Tennessee. Historic indigenous groups are known to have, and still do into the present-day, make and use turtle shell rattles in the region. Ultimately, we determined that "food refuse" should not be the default interpretation of fragmentary box turtle remains, and instead the taphonomic history and contextual associations must be considered in full. The experimental process of crafting turtle shell rattles enhances our understanding of an ancient musical instrument and the success rate of identifying musical artifacts and distinguishing between other modified turtle remains in the archaeological record. This study expands our knowledge of ancient music in North America and prompts re-analysis of curated turtle remains in museums for rattlerelated modifications. Show less

Objectives To examine whether differential exposure to pre- and perinatal risk factors explained differences in levels of self-regulation between children of different races (White, Black, Hispanic, Asian, and Other). Methods Multiple regression models based on data from the Early Childhood Longitudinal Study, Birth Cohort (n approximate to 9,850) were used to analyze the impact of pre- and perinatal risk factors on the development of self-regulation at age 2 years. Results Racial differences... Show moreObjectives To examine whether differential exposure to pre- and perinatal risk factors explained differences in levels of self-regulation between children of different races (White, Black, Hispanic, Asian, and Other). Methods Multiple regression models based on data from the Early Childhood Longitudinal Study, Birth Cohort (n approximate to 9,850) were used to analyze the impact of pre- and perinatal risk factors on the development of self-regulation at age 2 years. Results Racial differences in levels of self-regulation were observed. Racial differences were also observed for 9 of the 12 pre-/perinatal risk factors. Multiple regression analyses revealed that a portion of the racial differences in self-regulation was explained by differential exposure to several of the pre-/perinatal risk factors. Specifically, maternal age at childbirth, gestational timing, and the family's socioeconomic status were significantly related to the child's level of self-regulation. These factors accounted for a statistically significant portion of the racial differences observed in self-regulation. Conclusions The findings indicate racial differences in self-regulation may be, at least partially, explained by racial differences in exposure to pre- and perinatal risk factors. Show less

Cardiac troponin C (cTnC) is a key effector in cardiac muscle excitation-contraction coupling as the Ca2+ sensing subunit responsible for controlling contraction. In this study, we generated several FRET sensors for divalent cations based on cTnC flanked by a donor fluorescent protein (CFP) and an acceptor fluorescent protein (YFP). The sensors report Ca2+ and Mg2+ binding, and relay global structural information about the structural relationship between cTnC's N- and C-domains. The sensors... Show moreCardiac troponin C (cTnC) is a key effector in cardiac muscle excitation-contraction coupling as the Ca2+ sensing subunit responsible for controlling contraction. In this study, we generated several FRET sensors for divalent cations based on cTnC flanked by a donor fluorescent protein (CFP) and an acceptor fluorescent protein (YFP). The sensors report Ca2+ and Mg2+ binding, and relay global structural information about the structural relationship between cTnC's N- and C-domains. The sensors were first characterized using end point titrations to decipher the response to Ca2+ binding in the presence or absence of Mg2+. The sensor that exhibited the largest responses in end point titrations, CTV-TnC, (Cerulean, TnC, and Venus) was characterized more extensively. Most of the divalent cation-dependent FRET signal originates from the high affinity C-terminal EF hands. CTV-TnC reconstitutes into skinned fiber preparations indicating proper assembly of troponin complex, with only similar to 0.2 pCa unit rightward shift of Ca2+-sensitive force development compared to WT-cTnC. Affinity of CTV-TnC for divalent cations is in agreement with known values for WT-cTnC. Analytical ultracentrifugation indicates that CTV-TnC undergoes compaction as divalent cations bind. C-terminal sites induce ion-specific (Ca2+ versus Mg2+) conformational changes in cTnC. Our data also provide support for the presence of additional, non-EF-hand sites on cTnC for Mg2+ binding. In conclusion, we successfully generated a novel FRET-Ca2+ sensor based on full length cTnC with a variety of cellular applications. Our sensor reveals global structural information about cTnC upon divalent cation binding. Show less

Introduction Approximately 20 million new sexually transmitted infections (STIs) are diagnosed yearly in the United States costing the healthcare system an estimated $16 billion in direct medical expenses. The presence of other STIs increases the risk of HIV transmission. The Centers for Disease Control and Prevention (CDC) has long recommended routine HIV screening for individuals with a diagnosed STI. Unfortunately, HIV screening prevalence among STI diagnosed patients are still sub-optimal... Show moreIntroduction Approximately 20 million new sexually transmitted infections (STIs) are diagnosed yearly in the United States costing the healthcare system an estimated $16 billion in direct medical expenses. The presence of other STIs increases the risk of HIV transmission. The Centers for Disease Control and Prevention (CDC) has long recommended routine HIV screening for individuals with a diagnosed STI. Unfortunately, HIV screening prevalence among STI diagnosed patients are still sub-optimal in many healthcare settings. Objective To determine the proportion of STI-diagnosed persons in the Medicaid population who are screened for HIV, examine correlates of HIV screening, and to suggest critical intervention points to increase HIV screening in this population. Methods A retrospective database analysis was conducted to examine the prevalence and correlates of HIV screening among participants. Participant eligibility was restricted to Medicaid enrollees in 29 states with a primary STI diagnosis (chlamydia, gonorrhea, and syphilis) or pelvic inflammatory disease claim in 2009. HIV-positive persons were excluded from the study. Frequencies and descriptive statistics were conducted to characterize the sample in general and by STI diagnosis. Univariate and multivariate logistic regression were performed to estimate unadjusted odds ratios and adjusted odds ratio respectively and the 95% confidence intervals. Multivariate logistic regression models that included the independent variables (race, STI diagnosis, and healthcare setting) and covariates (gender, residential status, age, and state) were analyzed to examine independent associations with HIV screening. Results About 43% of all STI-diagnosed study participants were screened for HIV. STI-diagnosed persons that were between 20-24 years, female, residing in a large metropolitan area and with a syphilis diagnosis were more likely to be screened for HIV. Participants who received their STI diagnosis in the emergency department were less likely to be screened for HIV than those diagnosed in a physician's office. Conclusion This study showed that HIV screening prevalence among persons diagnosed with an STI are lower than expected based on the CDC's recommendations. These suboptimal HIV screening prevalence present "missed opportunities" for HIV screening in at-risk populations. Measures and incentives to increase HIV screening among all STI-diagnosed persons are vital to the timely identification of HIV infection, linkage to HIV care, and mitigating further HIV transmission. Show less

Neighboring plants can decrease or increase each other's likelihood of damage from herbivores through associational resistance or susceptibility, respectively. Associational effects (AE) can transpire through changes in herbivore or plant traits that affect herbivore movement, densities, and feeding behaviors to ultimately affect plant damage. While much work has focused on understanding the mechanisms that underlie associational effects, we know little about how these mechanisms are... Show moreNeighboring plants can decrease or increase each other's likelihood of damage from herbivores through associational resistance or susceptibility, respectively. Associational effects (AE) can transpire through changes in herbivore or plant traits that affect herbivore movement, densities, and feeding behaviors to ultimately affect plant damage. While much work has focused on understanding the mechanisms that underlie associational effects, we know little about how these mechanisms are influenced by neighborhood composition, i.e., plant density or relative frequency which is necessary to make predictions about when AE should occur in nature. Using a series of field and greenhouse experiments, I examined how plant density and relative frequency affected plant damage to Solanum carolinense and four mechanisms that underlie AE; (i) accumulation of insect herbivores and arthropod predators, (ii) microclimate conditions, (iii) plant resistance, and (iv) specialist herbivore preference. I found a positive relationship between S. carolinense damage and the relative frequency of a non-focal neighbor (Solidago altissima) and all four AE mechanisms were influenced by one or multiple neighborhood components. Frequency-dependence in S. carolinense damage is most likely due to greater generalist herbivore load on S. carolinense (through spillover from S. altissima) with microclimate variables, herbivore preference, predation pressures, and plant resistance having relatively weaker effects. Associational effects may have long-term consequences for these two plant species during plant succession and understanding context-dependent herbivory has insect pest management implication for other plant species in agriculture and forestry. Show less

Date Issued

2017-05-09

Identifier

FSU_libsubv1_wos_000401314000013, 10.1371/journal.pone.0176499

Format

Citation

Title

Impacts Of The Deepwater Horizon Oil Spill Evaluated Using An End-to-end Ecosystem Model.

We use a spatially explicit biogeochemical end-to-end ecosystem model, Atlantis, to simulate impacts from the Deepwater Horizon oil spill and subsequent recovery of fish guilds. Dose-response relationships with expected oil concentrations were utilized to estimate the impact on fish growth and mortality rates. We also examine the effects of fisheries closures and impacts on recruitment. We validate predictions of the model by comparing population trends and age structure before and after the... Show moreWe use a spatially explicit biogeochemical end-to-end ecosystem model, Atlantis, to simulate impacts from the Deepwater Horizon oil spill and subsequent recovery of fish guilds. Dose-response relationships with expected oil concentrations were utilized to estimate the impact on fish growth and mortality rates. We also examine the effects of fisheries closures and impacts on recruitment. We validate predictions of the model by comparing population trends and age structure before and after the oil spill with fisheries independent data. The model suggests that recruitment effects and fishery closures had little influence on biomass dynamics. However, at the assumed level of oil concentrations and toxicity, impacts on fish mortality and growth rates were large and commensurate with observations. Sensitivity analysis suggests the biomass of large reef fish decreased by 25% to 50% in areas most affected by the spill, and biomass of large demersal fish decreased even more, by 40% to 70%. Impacts on reef and demersal forage caused starvation mortality in predators and increased reliance on pelagic forage. Impacts on the food web translated effects of the spill far away from the oiled area. Effects on age structure suggest possible delayed impacts on fishery yields. Recovery of high-turnover populations generally is predicted to occur within 10 years, but some slower-growing populations may take 30+ years to fully recover. Show less

The reconcilability of actions and beliefs in inter-country relationships, either in business or politics, is of vital importance as incorrect beliefs on foreigners' behavior can have serious implications. We study a typical inter-country interaction by means of a controlled laboratory investment game experiment in Germany, Israel and Palestine involving 400 student participants in total. An investor has to take a risky decision in a foreign country that involves transferring money to an... Show moreThe reconcilability of actions and beliefs in inter-country relationships, either in business or politics, is of vital importance as incorrect beliefs on foreigners' behavior can have serious implications. We study a typical inter-country interaction by means of a controlled laboratory investment game experiment in Germany, Israel and Palestine involving 400 student participants in total. An investor has to take a risky decision in a foreign country that involves transferring money to an investee/allocator. We found a notable constellation of calibrated and un-calibrated beliefs. Within each country, transfer standards exist, which investees correctly anticipate within their country. However, across countries these standards differ. By attributing the standard of their own environment to the other countries investees are remarkably bad in predicting foreign investors' behavior. The tendency to ignore this potential difference can be a source of misinterpreting motives in cross-country interaction. Foreigners might perceive behavior as unfavorable or favorable differentiation, even thoughunknown to them-investors actually treat fellow-country people and foreigners alike. Show less

Date Issued

2016-06-16

Identifier

FSU_libsubv1_wos_000378029800025, 10.1371/journal.pone.0156998

Format

Citation

Title

Incidence Of Diabetes Mellitus And Obesity And The Overlap Of Comorbidities In Hiv Plus Hispanics Initiating Antiretroviral Therapy.

Background Cardiovascular disease (CVD) is a leading health threat for HIV+ patients on antiretroviral therapy (ART); cardiometabolic comorbidities are key predictors of risk. Data are limited on incidence of metabolic comorbidities in HIV+ individuals initiating ART in low and middle income countries (LMICs), particularly for Hispanics. We examined incidence of diabetes and obesity in a prospective cohort of those initiating ART in the Dominican Republic. Methods Participants >= 18 years,... Show moreBackground Cardiovascular disease (CVD) is a leading health threat for HIV+ patients on antiretroviral therapy (ART); cardiometabolic comorbidities are key predictors of risk. Data are limited on incidence of metabolic comorbidities in HIV+ individuals initiating ART in low and middle income countries (LMICs), particularly for Hispanics. We examined incidence of diabetes and obesity in a prospective cohort of those initiating ART in the Dominican Republic. Methods Participants >= 18 years, initiating ART <90 days prior to study enrollment, were examined for incidence of impaired fasting glucose (IFG), diabetes mellitus (DM), overweight, and obesity. Fasting plasma glucose (FPG) 100-125mg/dl defined IFG; FPG >= 126 mg/dl, diagnosis per medical record, or use of hypoglycemic medication defined DM. Overweight and obesity were BMI 25-30 and >= 30kg/m2, respectively. Dyslipidemia was total cholesterol >= 240mg/dl or use of lipid-lowering medication. Framingham risk equation was used to determine ten-year CVD risk at the end of observation. Results Of 153 initiating ART, 8 (6%) had DM and 23 (16%) had IFG at baseline, 6 developed DM (28/1000 person-years follow up [PYFU]) and 46 developed IFG (329/1000 PYFU). At baseline, 24 (18%) were obese and 36 (27%) were overweight, 15 became obese (69/1000 PYFU) and 22 became overweight (163/1000 PYFU). Median observation periods for the diabetes and obesity analyses were 23.5 months and 24.3 months, respectively. Increased CVD risk (>= 10% 10-year Framingham risk score) was present for 13% of the cohort; 79% of the cohort had >= 1 cardiometabolic comorbidity, 48% had >= 2, and 13% had all three. Conclusions In this Hispanic cohort in an LMIC, incidences of IFG/DM and overweight/obesity were similar to or higher than that found in high income countries, and cardiometabolic disorders affected three-quarters of those initiating ART. Care models incorporating cardiovascular risk reduction into HIV treatment programs are needed to prevent CVD-associated mortality in this vulnerable population. Show less

Date Issued

2016-08-10

Identifier

FSU_libsubv1_wos_000381380400055, 10.1371/journal.pone.0160797

Format

Citation

Title

Influence Of Repressive Histone And Dna Methylation Upon D4z4 Transcription In Non-myogenic Cells.

Creator

Das, Sunny, Chadwick, Brian P.

Abstract/Description

We looked at a disease-associated macrosatellite array D4Z4 and focused on epigenetic factors influencing its chromatin state outside of the disease-context. We used the HCT116 cell line that contains the non-canonical polyadenylation (poly-A) signal required to stabilize somatic transcripts of the human double homeobox gene DUX4, encoded from D4Z4. In HCT116, D4Z4 is packaged into constitutive heterochromatin, characterized by DNA methylation and histone H3 tri-methylation at lysine 9 ... Show moreWe looked at a disease-associated macrosatellite array D4Z4 and focused on epigenetic factors influencing its chromatin state outside of the disease-context. We used the HCT116 cell line that contains the non-canonical polyadenylation (poly-A) signal required to stabilize somatic transcripts of the human double homeobox gene DUX4, encoded from D4Z4. In HCT116, D4Z4 is packaged into constitutive heterochromatin, characterized by DNA methylation and histone H3 tri-methylation at lysine 9 (H3K9me3), resulting in low basal levels of D4Z4-derived transcripts. However, a double knockout (DKO) of DNA methyltransferase genes, DNMT1 and DNMT3B, but not either alone, results in significant loss of DNA and H3K9 methylation. This is coupled with upregulation of transcript levels from the array, including DUX4 isoforms (DUX4-fl) that are abnormally expressed in somatic muscle in the disease Facioscapulohumeral muscular dystrophy (FSHD) along with DUX4 protein, as indicated indirectly by upregulation of bondafide targets of DUX4 in DKO but not HCT116 cells. Results from treatment with a chemical inhibitor of histone methylation in HCT116 suggest that in the absence of DNA hypomethylation, H3K9me3 loss alone is sufficient to facilitate DUX4-fl transcription. Additionally, characterization of a cell line from a patient with Immunodeficiency, Centromeric instability and Facial anomalies syndrome 1 (ICF1) possessing a non-canonical poly-A signal and DNA hypomethylation at D4Z4 showed DUX4 target gene upregulation in the patient when compared to controls in spite of retention of H3K9me3. Taken together, these data suggest that both DNA methylation and H3K9me3 are determinants of D4Z4 silencing. Moreover, we show that in addition to testis, there is appreciable expression of spliced and polyadenylated D4Z4 derived transcripts that contain the complete DUX4 open reading frame (ORF) along with DUX4 target gene expression in the thymus, suggesting that DUX4 may provide normal function in this somatic tissue. Show less

Date Issued

2016-07-28

Identifier

FSU_libsubv1_wos_000381516100091, 10.1371/journal.pone.0160022

Format

Citation

Title

Interactive Effects Of Precipitation And Nitrogen Enrichment On Multi-trophic Dynamics In Plant-arthropod Communities.

Creator

Griffith, Kaitlin A., Grinath, Joshua B.

Abstract/Description

Patterns of precipitation and nitrogen (N) deposition are changing in ecosystems worldwide. Simultaneous increases in precipitation and N deposition can relieve co-limiting soil resource conditions for plants and result in synergistic plant responses, which may affect animals and plant responses to higher trophic levels. However, the potential for synergistic effects of precipitation and N deposition on animals and plant responses to herbivores and predators (via trophic cascades) is unclear.... Show morePatterns of precipitation and nitrogen (N) deposition are changing in ecosystems worldwide. Simultaneous increases in precipitation and N deposition can relieve co-limiting soil resource conditions for plants and result in synergistic plant responses, which may affect animals and plant responses to higher trophic levels. However, the potential for synergistic effects of precipitation and N deposition on animals and plant responses to herbivores and predators (via trophic cascades) is unclear. We investigated the influence of precipitation and N enrichment on ecological dynamics across three trophic levels, hypothesizing that herbivores and plants would exhibit synergistic responses to the combined influence of precipitation, N amendments and predators. To test this, we conducted a field experiment with arthropods on two model plant species, Nicotiana tabacum and Nicotiana rustica. First, we characterized the plant-arthropod assemblages, finding that N.tabacum hosted greater abundances of caterpillars, while N. rustica hosted more sap-sucking herbivores. Next, we evaluated the effects of rainwater, soil N, and predatory spider manipulations for both plantarthropod assemblages. On N. tabacum, water and N availability had an interactive effect on caterpillars, where caterpillars were most abundant with rainwater additions and least abundant when both rainwater and N were added. For N. rustica, foliar chemistry had a synergistic response to all three experimental factors. Compared to spider-absent conditions, leaf N concentration increased and C/N decreased when spiders were present, but this response only occurred under high water and N availability. Spiders indirectly altered plant chemistry via a facilitative effect of spiders on sap-sucking herbivores, potentially due to intra-guild predation, and a positive effect of sap-suckers on foliar N concentration. Our study suggests that predictions of the ecological impacts of altered precipitation and N deposition may need to account for the effects of resource co-limitation on dynamics across trophic levels. Show less

Stable carbon and nitrogen isotope values (delta C-13 and delta N-15) were used to evaluate trophic niche overlap between two filter-feeding fishes (known together as bigheaded carp) native to China, silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis), and three native filter-feeding fish including bigmouth buffalo (Ictiobus cyprinellus), gizzard shad (Dorosoma cepedianum) and paddlefish (Polyodon spathula) in the lower Missouri River, USA, using the... Show moreStable carbon and nitrogen isotope values (delta C-13 and delta N-15) were used to evaluate trophic niche overlap between two filter-feeding fishes (known together as bigheaded carp) native to China, silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis), and three native filter-feeding fish including bigmouth buffalo (Ictiobus cyprinellus), gizzard shad (Dorosoma cepedianum) and paddlefish (Polyodon spathula) in the lower Missouri River, USA, using the Bayesian Stable Isotope in R statistics. Results indicate that except for bigmouth buffalo, all species displayed similar trophic niche size and trophic diversity. Bigmouth buffalo occupied a small trophic niche and had the greatest trophic overlap with silver carp (93.6%) and bighead carp (94.1%) followed by gizzard shad (91.0%). Paddlefish had a trophic niche which relied on some resources different from those used by other species, and therefore had the lowest trophic overlap with bigheaded carp and other two native fish. The trophic overlap by bigheaded carp onto native fish was typically stronger than the reverse effects from native fish. Average niche overlap between silver carp and native species was as high as 71%, greater than niche overlap between bighead carp and native fish (64%). Our findings indicate that bigheaded carps are a potential threat to a diverse and stable native fish community. Show less

Date Issued

2018-05-21

Identifier

FSU_libsubv1_wos_000432537100033, 10.1371/journal.pone.0197584

Format

Citation

Title

A Landmark-Free Method for Three-Dimensional Shape Analysis.

Creator

Pomidor, Benjamin J., Makedonska, Jana, Slice, Dennis E.

Abstract/Description

Background The tools and techniques used in morphometrics have always aimed to transform the physical shape of an object into a concise set of numerical data for mathematical analysis. The advent of landmark-based morphometrics opened new avenues of research, but these methods are not without drawbacks. The time investment required of trained individuals to accurately landmark a data set is significant, and the reliance on readily-identifiable physical features can hamper research efforts.... Show moreBackground The tools and techniques used in morphometrics have always aimed to transform the physical shape of an object into a concise set of numerical data for mathematical analysis. The advent of landmark-based morphometrics opened new avenues of research, but these methods are not without drawbacks. The time investment required of trained individuals to accurately landmark a data set is significant, and the reliance on readily-identifiable physical features can hamper research efforts. This is especially true of those investigating smooth or featureless surfaces. Methods In this paper, we present a new method to perform this transformation for data obtained from high-resolution scanning technology. This method uses surface scans, instead of landmarks, to calculate a shape difference metric analogous to Procrustes distance and perform superimposition. This is accomplished by building upon and extending the Iterative Closest Point algorithm. We also explore some new ways this data can be used; for example, we can calculate an averaged surface directly and visualize point-wise shape information over this surface. Finally, we briefly demonstrate this method on a set of primate skulls and compare the results of the new methodology with traditional geometric morphometric analysis. Show less

Some have explained large sex differences in visuospatial abilities by genetic adaptations to different roles in primitive hunter-gatherer societies and the interaction of innate biological differences and environmental factors. We explored the extent to which variations in behavior and acquired skills can provide alternative accounts for sex differences in the performance of a complex spatially-demanding video game (Space Fortress). Men and women with limited video game experience were given... Show moreSome have explained large sex differences in visuospatial abilities by genetic adaptations to different roles in primitive hunter-gatherer societies and the interaction of innate biological differences and environmental factors. We explored the extent to which variations in behavior and acquired skills can provide alternative accounts for sex differences in the performance of a complex spatially-demanding video game (Space Fortress). Men and women with limited video game experience were given 30 hours of training, and latent curve analyses examined the development of their ship control performance and behavior. Men had significantly better control performance than women before and after training, but differences diminished substantially over the training period. An analysis of participants' joystick behaviors revealed that initially men and women relied on different patterns of control behaviors, but changes in these behaviors over time accounted for the reduced sex differences in performance. When we controlled for these differences in behavior, sex effects after training were no longer significant. Finally, examining the development of control performance and control behaviors of men and women categorized as initially high and low performers revealed the lower-performing women may have been controlling their ship using an approach that was very different from the men and higher-performing women. The potential problems of analyzing men and women's spatial performance as homogenous groups are discussed, as well as how these issues may account for sex differences in skilled video game performance and perhaps other domains involving spatial abilities. Show less

Date Issued

2018-05-30

Identifier

FSU_libsubv1_wos_000433634800028, 10.1371/journal.pone.0197311

Format

Citation

Title

Magmatic Evolution Of Panama Canal Volcanic Rocks: A Record Of Arc Processes And Tectonic Change.

Social media analysis has shown tremendous potential to understand public's opinion on a wide variety of topics. In this paper, we have mined Twitter to understand the public's perception of the Internet of Things (IoT). We first generated the discussion trends of the IoT from multiple Twitter data sources and validated these trends with Google Trends. We then performed sentiment analysis to gain insights of the public's attitude towards the IoT. As anticipated, our analysis indicates that... Show moreSocial media analysis has shown tremendous potential to understand public's opinion on a wide variety of topics. In this paper, we have mined Twitter to understand the public's perception of the Internet of Things (IoT). We first generated the discussion trends of the IoT from multiple Twitter data sources and validated these trends with Google Trends. We then performed sentiment analysis to gain insights of the public's attitude towards the IoT. As anticipated, our analysis indicates that the public's perception of the IoT is predominantly positive. Further, through topic modeling, we learned that public tweets discussing the IoT were often focused on business and technology. However, the public has great concerns about privacy and security issues toward the IoT based on the frequent appearance of related terms. Nevertheless, no unexpected perceptions were identified through our analysis. Our analysis was challenged by the limited fraction of tweets relevant to our study. Also, the user demographics of Twitter users may not be strongly representative of the population of the general public. Show less

Date Issued

2016-07-08

Identifier

FSU_libsubv1_wos_000380005400060, 10.1371/journal.pone.0158450

Format

Citation

Title

Multi-stage Optimization Of A Deep Model: A Case Study On Ground Motion Modeling.

In this study, a multi-stage optimization procedure is proposed to develop deep neural network models which results in a powerful deep learning pipeline called intelligent deep learning (iDeepLe). The proposed pipeline is then evaluated by a challenging real-world problem, the modeling of the spectral acceleration experienced by a particle during earthquakes. This approach has three main stages to optimize the deep model topology, the hyper-parameters, and its performance, respectively. This... Show moreIn this study, a multi-stage optimization procedure is proposed to develop deep neural network models which results in a powerful deep learning pipeline called intelligent deep learning (iDeepLe). The proposed pipeline is then evaluated by a challenging real-world problem, the modeling of the spectral acceleration experienced by a particle during earthquakes. This approach has three main stages to optimize the deep model topology, the hyper-parameters, and its performance, respectively. This pipeline optimizes the deep model via adaptive learning rate optimization algorithms for both accuracy and complexity in multiple stages, while simultaneously solving the unknown parameters of the regression model. Among the seven adaptive learning rate optimization algorithms, Nadam optimization algorithm has shown the best performance results in the current study. The proposed approach is shown to be a suitable tool to generate solid models for this complex real-world system. The results also show that the parallel pipeline of iDeepLe has the capacity to handle big data problems as well. Show less

Oceanographic field programs often use delta N-15 biogeochemical measurements and in situ rate measurements to investigate nitrogen cycling and planktonic ecosystem structure. However, integrative modeling approaches capable of synthesizing these distinct measurement types are lacking. We develop a novel approach for incorporating delta N-15 isotopic data into existing Markov Chain Monte Carlo (MCMC) random walk methods for solving linear inverse ecosystem models. We test the ability of this... Show moreOceanographic field programs often use delta N-15 biogeochemical measurements and in situ rate measurements to investigate nitrogen cycling and planktonic ecosystem structure. However, integrative modeling approaches capable of synthesizing these distinct measurement types are lacking. We develop a novel approach for incorporating delta N-15 isotopic data into existing Markov Chain Monte Carlo (MCMC) random walk methods for solving linear inverse ecosystem models. We test the ability of this approach to recover food web indices (nitrate uptake, nitrogen fixation, zooplankton trophic level, and secondary production) derived from forward models simulating the planktonic ecosystems of the California Current and Amazon River Plume. We show that the MCMC with delta N-15 approach typically does a better job of recovering ecosystem structure than the standard MCMC or L-2 minimum norm (L2MN) approaches, and also outperforms an L2MN with delta N-15 approach. Furthermore, we find that the MCMC with delta N-15 approach is robust to the removal of input equations and hence is well suited to typical pelagic ecosystem studies for which the system is usually vastly under-constrained. Our approach is easily extendable for use with delta C-13 isotopic measurements or variable carbon:nitrogen stoichiometry. Show less

Racial disparities persist in adverse perinatal outcomes such as preterm birth, low birthweight (LBW), and infant mortality across the U.S. Although pervasive, these disparities are not universal. Some communities have experienced significant improvements in black (or African American) birth outcomes, both in absolute rates and in rate ratios relative to whites. This study assessed county-level progress on trends in black and white LBW rates as an indicator of progress toward more equal birth... Show moreRacial disparities persist in adverse perinatal outcomes such as preterm birth, low birthweight (LBW), and infant mortality across the U.S. Although pervasive, these disparities are not universal. Some communities have experienced significant improvements in black (or African American) birth outcomes, both in absolute rates and in rate ratios relative to whites. This study assessed county-level progress on trends in black and white LBW rates as an indicator of progress toward more equal birth outcomes for black infants. County-level LBW data were obtained from the 2003 to 2013 U.S. Natality files. Black LBW rates, black-white rate ratios and percent differences over time were calculated. Trend lines were first assessed for significant differences in slope (i.e., converging, diverging, or parallel trend lines). For counties with parallel trend lines, intercepts were tested for statistically significant differences (sustained equality vs. persistent disparities). To assess progress, black LBW rates were compared to white LBW rates, and the trend lines were tested for significant decline. Each county's progress toward black-white equality was ultimately categorized into five possible trend patterns (n = 408): (1) converging LBW rates with reductions in the black LBW rate (decreasing disparities, n = 4, 1 %); (2) converging LBW rates due to worsening white LBW rates (n = 5, 1 %); (3) diverging LBW rates (increasing disparities, n = 9, 2%); (4) parallel LBW rates (persistent disparities, n = 373, 91%); and (5) overlapping trend lines (sustained equality, n = 18, 4%). Only four counties demonstrated improvement toward equality with decreasing black LBW rates. There is significant county-level variation in progress toward racial equality in adverse birth outcomes such as low birthweight. Still, some communities are demonstrating that more equitable outcomes are possible. Further research is needed in these positive exemplar communities to identify what works in accelerating progress toward more equal birth outcomes. Show less

Date Issued

2018-07-31

Identifier

FSU_libsubv1_wos_000440300500056, 10.1371/journal.pone.0201658

Format

Citation

Title

Practices Of Research Data Curation In Institutional Repositories: A Qualitative View From Repository Staff.

Creator

Lee, Dong Joon, Stvilia, Besiki

Abstract/Description

The importance of managing research data has been emphasized by the government, funding agencies, and scholarly communities. Increased access to research data increases the impact and efficiency of scientific activities and funding. Thus, many research institutions have established or plan to establish research data curation services as part of their Institutional Repositories (IRs). However, in order to design effective research data curation services in IRs, and to build active research... Show moreThe importance of managing research data has been emphasized by the government, funding agencies, and scholarly communities. Increased access to research data increases the impact and efficiency of scientific activities and funding. Thus, many research institutions have established or plan to establish research data curation services as part of their Institutional Repositories (IRs). However, in order to design effective research data curation services in IRs, and to build active research data providers and user communities around those IRs, it is essential to study current data curation practices and provide rich descriptions of the sociotechnical factors and relationships shaping those practices. Based on 13 interviews with 15 IR staff members from 13 large research universities in the United States, this paper provides a rich, qualitative description of research data curation and use practices in IRs. In particular, the paper identifies data curation and use activities in IRs, as well as their structures, roles played, skills needed, contradictions and problems present, solutions sought, and workarounds applied. The paper can inform the development of best practice guides, infrastructure and service templates, as well as education in research data curation in Library and Information Science (LIS) schools. Show less

Date Issued

2017-03-16

Identifier

FSU_libsubv1_wos_000396318300105, 10.1371/journal.pone.0173987

Format

Citation

Title

Researchers' Participation In And Motivations For Engaging With Research Information Management Systems.

Creator

Stvilia, Besiki, Wu, Shuheng, Lee, Dong Joon

Abstract/Description

Researchers' participation in online RIMSs This article examined how researchers participated in research information management systems (RIMSs), their motivations for participation, and their priorities for those motivations. Profile maintenance, question-answering, and endorsement activities were used to define three cumulatively increasing levels of participation: Readers, Record Managers, and Community Members. Junior researchers were more engaged in RIMSs than were senior researchers.... Show moreResearchers' participation in online RIMSs This article examined how researchers participated in research information management systems (RIMSs), their motivations for participation, and their priorities for those motivations. Profile maintenance, question-answering, and endorsement activities were used to define three cumulatively increasing levels of participation: Readers, Record Managers, and Community Members. Junior researchers were more engaged in RIMSs than were senior researchers. Postdocs had significantly higher odds of endorsing other researchers for skills and being categorized as Community Members than did full and associate professors. Assistant professors were significantly more likely to be Record Managers than were members of any other seniority categories. Finally, researchers from the life sciences showed a significantly higher propensity for being Community Members than Readers and Record Managers when compared with researchers from engineering and the physical sciences, respectively. Researchers' motivations to participate in RIMSs When performing activities, researchers were motivated by the desire to share scholarship, feel competent, experience a sense of enjoyment, improve their status, and build ties with other members of the community. Moreover, when researchers performed activities that directly benefited other members of a RIMS, they assigned higher priorities to intrinsic motivations, such as perceived self-efficacy, enjoyment, and building community ties. Researchers at different stages of their academic careers and disciplines ranked some of the motivations for engaging with RIMSs differently. The general model of research participation in RIMSs; the relationships among RIMS activities; the motivation scales for activities; and the activity, seniority, and discipline-specific priorities for the motivations developed by this study provide the foundation for a framework for researcher participation in RIMSs. This framework can be used by RIMSs and institutional repositories to develop tools and design mechanisms to increase researchers' engagement in RIMSs. Show less

A popular objective criterion for partitioning a set of actors into core and periphery subsets is the maximization of the correlation between an ideal and observed structure associated with intra-core and intra-periphery ties. The resulting optimization problem has commonly been tackled using heuristic procedures such as relocation algorithms, genetic algorithms, and simulated annealing. In this paper, we present a computationally efficient simulated annealing algorithm for maximum... Show moreA popular objective criterion for partitioning a set of actors into core and periphery subsets is the maximization of the correlation between an ideal and observed structure associated with intra-core and intra-periphery ties. The resulting optimization problem has commonly been tackled using heuristic procedures such as relocation algorithms, genetic algorithms, and simulated annealing. In this paper, we present a computationally efficient simulated annealing algorithm for maximum correlation core/periphery partitioning of binary networks. The algorithm is evaluated using simulated networks consisting of up to 2000 actors and spanning a variety of densities for the intra-core, intra-periphery, and inter-core-periphery components of the network. Core/periphery analyses of problem solving, trust, and information sharing networks for the frontline employees and managers of a consumer packaged goods manufacturer are provided to illustrate the use of the model. Show less

Date Issued

2017-05-09

Identifier

FSU_libsubv1_wos_000401314000001, 10.1371/journal.pone.0170448

Format

Citation

Title

Spatial And Temporal Variation In The Effects Of Climatic Variables On Dugong Calf Production.

Knowledge of the relationships between environmental forcing and demographic parameters is important for predicting responses from climatic changes and to manage populations effectively. We explore the relationships between the proportion of sea cows (Dugong dugon) classified as calves and four climatic drivers (rainfall anomaly, Southern Oscillation El Nino Index [SOI], NINO 3.4 sea surface temperature index, and number of tropical cyclones) at a range of spatially distinct locations in... Show moreKnowledge of the relationships between environmental forcing and demographic parameters is important for predicting responses from climatic changes and to manage populations effectively. We explore the relationships between the proportion of sea cows (Dugong dugon) classified as calves and four climatic drivers (rainfall anomaly, Southern Oscillation El Nino Index [SOI], NINO 3.4 sea surface temperature index, and number of tropical cyclones) at a range of spatially distinct locations in Queensland, Australia, a region with relatively high dugong density. Dugong and calf data were obtained from standardized aerial surveys conducted along the study region. A range of lagged versions of each of the focal climatic drivers (1 to 4 years) were included in a global model containing the proportion of calves in each population crossed with each of the lagged versions of the climatic drivers to explore relationships. The relative influence of each predictor was estimated via Gibbs variable selection. The relationships between the proportion of dependent calves and the climatic drivers varied spatially and temporally, with climatic drivers influencing calf counts at sub-regional scales. Thus we recommend that the assessment of and management response to indirect climatic threats on dugongs should also occur at sub-regional scales. Show less

Date Issued

2016-06-29

Identifier

FSU_libsubv1_wos_000378859400004, 10.1371/journal.pone.0155675

Format

Citation

Title

An Unusual Inverted Saline Microbial Mat Community in an Interdune Sabkha in the Rub' al Khali (the Empty Quarter), United Arab Emirates.

Salt flats (sabkha) are a recognized habitat for microbial life in desert environments and as analogs of habitats for possible life on Mars. Here we report on the physical setting and microbiology of interdune sabkhas among the large dunes in the Rub' al Khali (the Empty Quarter) in Liwa Oasis, United Arab Emirates. The salt flats, composed of gypsum and halite, are moistened by relatively fresh ground water. The result is a salinity gradient that is inverted compared to most salt flat... Show moreSalt flats (sabkha) are a recognized habitat for microbial life in desert environments and as analogs of habitats for possible life on Mars. Here we report on the physical setting and microbiology of interdune sabkhas among the large dunes in the Rub' al Khali (the Empty Quarter) in Liwa Oasis, United Arab Emirates. The salt flats, composed of gypsum and halite, are moistened by relatively fresh ground water. The result is a salinity gradient that is inverted compared to most salt flat communities with the hypersaline layer at the top and freshwater layers below. We describe and characterize a rich photosynthetically-based microbial ecosystem that is protected from the arid outside environment by a translucent salt crust. Gases collected from sediments under shallow ponds in the sabkha contain methane in concentrations as high as 3400 ppm. The salt crust could preserve biomarkers and other evidence for life in the salt after it dries out. Chloride-filled depressions have been identified on Mars and although surface flow of water is unlikely on Mars today, ground water is possible. Such a near surface system with modern groundwater flowing under ancient salt deposits could be present on Mars and could be accessed by surface rovers. Show less